Results: A procedure is introduced for quantitative representa-tion of MeSH annotations assigned to any group of articles (e.g articles for a specific gene). Similarity scores comparing MeSHOPs of genes and diseases successfully infer association of novel disease terms to genes, validated by future publications. Results indicate the number of papers for a gene or disease has a strong influence on predicted associations. Up to 16% improvement in predictive performance over baselines was obtained using MeSHOP comparisons.